The human genome program has been made possible, in part, by the ability to sort human chromosomes. Up to 2 fg of each of the 24 human chromosome types are being sorted for construction of chromosome-specific DNA libraries from a variety of cell types including primary euploid cell strains and somatic cell hybrids. Problems with chromosome recovery and maintenance of high molecular weight DNA have been resolved for applications involving YAC cloning. An exceptionally low rate of chimeras has been found in these flow sorted chromosome specific YAC libraries. Week-long continuous sorting experiments have been conducted to obtain sufficient material for cloning in large insert BAC libraries.